The ecological success of coral reef ecosystems is dependant on their obligate endosymbiosis with dinoflagellates in the family Symbiodiniaceae. This symbiosis does not occur in isolation; a diverse community of bacteria contribute to coral health and functioning. Though microbial-coral relationships are well studied, and dinoflagellate-bacterial associations are abundant in the marine environment, limited research focuses on Symbiodiniaceae-bacterial interactions. We combined autofluorescence quenching of Symbiodiniaceae with fluorescence in situ hybridisation to create three-dimensional reconstructions. These results present the first conclusive evidence that six species of Symbiodiniaceae harbour intracellular bacteria as well as cell surface associated extracellular bacteria. Hybridisation of class specific probes (Gammaproteobacteria, Alphaproteobacteria and Flavobacteriia) showed that taxonomic affiliation of intracellular bacteria differed between Symbiodiniaceae species. Furthermore, 147 members from the phyla Proteobacteria, Bacteroidetes and Firmicutes were isolated from ex hospite Symbiodiniaceae. Low diversity of cultured bacterial symbionts suggest that Symbiodiniaceae are selective in their association with bacteria. Based on the diversity and functional potential of Symbiodiniaceae-bacterial associations microbial interactions should no longer be ignored as potentially contributing to the coral holobiont health and functioning.